relsearch is open-source software for screening relatives between query and reference databases. The software is graphical-user-interface written in R language (>= 4.2.0) with GNU General Public License v3.0. It can be applied to autosomal short tandem repeat (STR) markers, Y-STR markers, and mitochondrial DNA sequences commonly used in forensic genetics. For autosomal STR markers, likelihood ratios (LRs) of each query-reference pair are calculated considering mutation and drop-out. For Y-STR markers and mitochondrial DNA sequences, the software investigates the number of inconsistencies between query and reference haplotypes.
Ensure that R (>= 4.2.0) is installed. It is available from the R Development Core Team website (http://www.R-project.org).
Begin an R session.
Install ‘devtools’ package by using the following command.
install.packages("devtools")
devtools::install_github("manabe0322/relsearch")
library(relsearch)
relsearch()
Fig. 1. Format of query database for autosomal STR
Note : format of query database
This file must include information regarding ‘Sample Name’ and each marker.
There are two columns in each marker.
The marker with two empty cells (e.g., vWA of sample ‘Q20’ in Fig. 1) is ignored when calculating the LR.
The marker with one empty cell (e.g., D16S539 of sample ‘Q11’ in Fig. 1) can be regarded as allelic drop-out depending on the setting ‘Drop-out of query genotypes’ (see section 3.4).
An example file named “str_query_example.csv” is located in the folder ‘examples’.
Fig. 2. Format of reference database for autosomal STR
Note : format of reference database
This file must include information regarding ‘Sample Name’, ‘Relationship’, and each marker.
There are two columns in each marker.
Names of the column ‘Relationship’ relate to those of relationships in the IBD probabilities (see section 3.6).
If the relationship is not identified, leave the cell blank. When calculating LRs, all relationships for which the IBD probabilities is defined are considered.
The marker with two empty cells is ignored when calculating the LR.
The marker with one empty cell or with two same alleles (e.g., D3S1358 of sample ‘R22’ in Fig. 2) is regarded as the homozygotes.
An example file named “str_ref_example.csv” is located in the folder ‘examples’.
Fig. 3. Format of allele frequencies for autosomal STR
Note : format of allele frequencies
This file must include information regarding ‘Allele’ and each marker.
An example file named “str_af_example.csv” is located in the folder ‘examples’.
Note : Drop-out of query genotypes
‘Not consider’ : When calculating the LR, the marker with one empty cell in a query or reference database is regarded as the homozygote. The marker with two empty cells is ignored (i.e., LR = 1).
‘Consider only in the case that one allele is designated’ : When calculating the LR, the marker with one empty cell in a query or reference database is regarded as both the homozygote (without drop-out) and the heterozygote (with drop-out). The marker with two empty cells is ignored (i.e., LR = 1).
‘Consider also in the case that two alleles in homozygotes are designated’ : When calculating the LR, the marker with two same alleles in a query or reference database is also regarded as both the homozygote (without drop-out) and the heterozygote (with drop-out).
Note :
Note : Default display
All query names
All reference names
All relationships
Likelihood ratio (LR) > 1
Descending order of LR
Fig. 4. Format of query database for Y-STR
Note : format of query database
This file must include information regarding ‘Sample Name’ and each marker.
There is one column in each marker.
In the marker with more than one allele, each allele must be separated by a comma (e.g., DYS385).
The marker with an empty cell (e.g., DYS390 of sample ‘Q10’ in Fig. 4) is regarded as the ‘ignored loci’.
An example file named “y_query_example.csv” is located in the folder ‘examples’.
Fig. 5. Format of reference database for Y-STR
Note : format of reference database
This file must include information regarding ‘Sample Name’ and each marker.
There is one column in each marker.
In the marker with more than one allele, each allele must be separated by a comma (e.g., DYS385).
An example file named “y_ref_example.csv” is located in the folder ‘examples’.
Note : Default display
All query names
All reference names
Number of inconsistent loci : 0 or 1
Number of ignored loci : 0 or 1
Ascending order of the number of inconsistent loci and the number of ignored loci
Fig. 6. Format of query database for mtDNA
Note : format of query database
This file must include information regarding ‘Sample Name’, ‘Range’, and ‘Haplotype’.
An example file named “mt_query_example.csv” is located in the folder ‘examples’.
Fig. 7. Format of reference database for mtDNA
Note : format of reference database
This file must include information regarding ‘Sample Name’, ‘Range’, and ‘Haplotype’.
An example file named “mt_ref_example.csv” is located in the folder ‘examples’.
Note : Default display
All query names
All reference names
Shared length > 300
Number of inconsistency : 0 or 1
Descending order of the shared length
Ascending order of the number of inconsistency